YMR_2_CalcWaterElev+QAQC

This Rmd file is intended to capture the processing workflow for AIMS PT data from YMR (Youngmeter Ranch).

It takes barometrically corrected PT data (waterHeight_m) and should produce the following output columns:

• waterLevel_m = adjusted water height relative to local datum
  • For all GP watersheds, we are using the streambed as the local datum
• waterDepth_m = water level relative to streambed.
• waterElevation_m = water level relative to sea level.
• wetdry = intepretation of whether the sensor is wet, dry, or bad/missing data (NA)
• QAQC = AIMS-specific QAQC codes.

One complicating factor is that the waterDepth_m field can be NA if the sensor is dry OR if there is missing/bad data. To interpret this, use the wetdry column.

Set up workspace

## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
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## Attaching package: 'zoo'
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## 
## The following objects are masked from 'package:base':
## 
##     as.Date, as.Date.numeric
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## 
## Rows: 35 Columns: 23
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (11): Region, Watershed, Site, Samplers, Date, pH, Connected?, Flowing?...
## dbl  (10): Temp (*C), Pressure (mmHg), DO (%), DO (mg/L), Specific Cond. (uS...
## time  (2): Time (CST), Time (UTC)
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

## [1] "EN201" "EN301" "ENM04" "ENM06" "ENM08" "ENM11"

ENM11 processing

load data

## Rows: 82248 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (3): siteId, sublocation, rep
## dbl  (4): tempC, sensorPressure_kPa, baroPressure_kPa, waterHeight_m
## dttm (1): datetime
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 101681 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (3): siteId, sublocation, rep
## dbl  (4): tempC, sensorPressure_kPa, baroPressure_kPa, waterHeight_m
## dttm (1): datetime
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

## [1] "ENM11 calculated offsets"

## [1] "SW = -0.04206"

## [1] "PI = -0.660804"

iterative cleaning and adjustments - step with lots of manual decisions

All interactive plots made during process will be commented out for knitting.

QAQC, save, and visualize

## 
##     D     Z    ZD  <NA> 
## 69063   632  2029 45165

## 
##     D     Z    ZD  <NA> 
## 73740   201  1936 10599

ENM08 processing

load data

## Rows: 101704 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (3): siteId, sublocation, rep
## dbl  (4): tempC, sensorPressure_kPa, baroPressure_kPa, waterHeight_m
## dttm (1): datetime
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 60555 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (3): siteId, sublocation, rep
## dbl  (4): tempC, sensorPressure_kPa, baroPressure_kPa, waterHeight_m
## dttm (1): datetime
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

## [1] "ENM08 calculated offsets"

## [1] "SW = -0.0914400000000002"

## [1] "PI = -0.734568"

iterative cleaning and adjustments - step with lots of manual decisions

All interactive plots made during process will be commented out for knitting.

QAQC, save, and visualize

## 
##     D     Z    ZD  <NA> 
## 34553   613   963 28654

## 
##     D     Z    ZD  <NA> 
## 81957   481  2271 32180

ENM06 processing

load data

## Rows: 82246 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (3): siteId, sublocation, rep
## dbl  (4): tempC, sensorPressure_kPa, baroPressure_kPa, waterHeight_m
## dttm (1): datetime
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 101700 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (3): siteId, sublocation, rep
## dbl  (4): tempC, sensorPressure_kPa, baroPressure_kPa, waterHeight_m
## dttm (1): datetime
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

## [1] "ENM06 calculated offsets"

## [1] "SW = -0.10668"

## [1] "PI = -0.566928"

iterative cleaning and adjustments - step with lots of manual decisions

All interactive plots made during process will be commented out for knitting.

QAQC, save, and visualize

## 
##     D     Z    ZD  <NA> 
## 28456  1931   745 85757

## 
##     D     T     Z    ZD    ZT  <NA> 
## 42831   200  1094  1150     1 41198

ENM04 processing

load data

## Rows: 101682 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (3): siteId, sublocation, rep
## dbl  (4): tempC, sensorPressure_kPa, baroPressure_kPa, waterHeight_m
## dttm (1): datetime
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 101692 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (3): siteId, sublocation, rep
## dbl  (4): tempC, sensorPressure_kPa, baroPressure_kPa, waterHeight_m
## dttm (1): datetime
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

## [1] "ENM04 calculated offsets"

## [1] "SW = -0.00914400000000004"

## [1] "PI = -0.679704"

iterative cleaning and adjustments - step with lots of manual decisions

All interactive plots made during process will be commented out for knitting.

QAQC, save, and visualize

## 
##     D     Z    ZD  <NA> 
## 41775  1262  1124 72728

## 
##     D     T     Z    ZD    ZT  <NA> 
## 60936   635  1026  1617     2 52673

EN301 processing

load data

## Rows: 101699 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (3): siteId, sublocation, rep
## dbl  (4): tempC, sensorPressure_kPa, baroPressure_kPa, waterHeight_m
## dttm (1): datetime
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 101691 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (3): siteId, sublocation, rep
## dbl  (4): tempC, sensorPressure_kPa, baroPressure_kPa, waterHeight_m
## dttm (1): datetime
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

## [1] "EN301 calculated offsets"

## [1] "SW = -0.140208"

## [1] "PI = -0.597408"

iterative cleaning and adjustments - step with lots of manual decisions

All interactive plots made during process will be commented out for knitting.

QAQC, save, and visualize

## 
##     D     Z    ZD  <NA> 
## 48845  1176  1332 65536

## 
##     D     T     Z    ZD    ZT  <NA> 
## 76311     1   459  1682     1 38435

EN201 processing

load data

## Rows: 101700 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (3): siteId, sublocation, rep
## dbl  (4): tempC, sensorPressure_kPa, baroPressure_kPa, waterHeight_m
## dttm (1): datetime
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 79988 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr  (3): siteId, sublocation, rep
## dbl  (4): tempC, sensorPressure_kPa, baroPressure_kPa, waterHeight_m
## dttm (1): datetime
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

## [1] "EN201 calculated offsets"

## [1] "SW = -0.402336"

## [1] "PI = -0.667512"

iterative cleaning and adjustments - step with lots of manual decisions

All interactive plots made during process will be commented out for knitting.

QAQC, save, and visualize

## 
##     D     Z    ZD  <NA> 
## 35597  1055  1016 79221

## 
##     D     Z    ZD  <NA> 
## 75947   609  2116 38217